[Vegan-commits] r938 - in pkg/vegan: R man

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2009-08-22 14:09:47 +0200 (Sat, 22 Aug 2009)
New Revision: 938

Modified:
   pkg/vegan/R/ordihull.R
   pkg/vegan/R/summary.ordihull.R
   pkg/vegan/man/ordihull.Rd
Log:
ordihull finds now centre of the points, and summary.ordihull the centre of the polygon instead of the centre of the vertices

Modified: pkg/vegan/R/ordihull.R
===================================================================
--- pkg/vegan/R/ordihull.R	2009-08-22 05:42:42 UTC (rev 937)
+++ pkg/vegan/R/ordihull.R	2009-08-22 12:09:47 UTC (rev 938)
@@ -22,7 +22,7 @@
                 ordiArgAbsorber(X[hpts, ], FUN = lines, ...)
             else ordiArgAbsorber(X[hpts,], FUN = polygon, ...)
             if (label) {
-                cntr <- colMeans(X[hpts[-1],])
+                cntr <- colMeans(X)
                 ordiArgAbsorber(cntr[1], cntr[2], labels = is,
                                 FUN = text, ...)
             }

Modified: pkg/vegan/R/summary.ordihull.R
===================================================================
--- pkg/vegan/R/summary.ordihull.R	2009-08-22 05:42:42 UTC (rev 937)
+++ pkg/vegan/R/summary.ordihull.R	2009-08-22 12:09:47 UTC (rev 938)
@@ -9,7 +9,18 @@
         else
             abs(sum(x[-n,1]*x[-1,2] - x[-1,1]*x[-n,2]))/2
     }
+    polycentre <- function(x) {
+        n <- nrow(x)
+        if (n < 4)
+            return(colMeans(x[-n,]))
+        xy <- x[-n,1]*x[-1,2] - x[-1,1]*x[-n,2]
+        A <- sum(xy)/2
+        xc <- sum((x[-n,1] + x[-1,1]) * xy)/A/6
+        yc <- sum((x[-n,2] + x[-1,2]) * xy)/A/6
+        structure(c(xc, yc), names = colnames(x))
+    }
     areas <- sapply(object, function(x) polyarea(x))
     cnts <- sapply(object, function(x) colMeans(x[-1,]))
-    rbind(cnts, `Area` = areas)
+    altcnts <- sapply(object, function(x) polycentre(x))
+    rbind(cnts, altcnts, `Area` = areas)
 }

Modified: pkg/vegan/man/ordihull.Rd
===================================================================
--- pkg/vegan/man/ordihull.Rd	2009-08-22 05:42:42 UTC (rev 937)
+++ pkg/vegan/man/ordihull.Rd	2009-08-22 12:09:47 UTC (rev 938)
@@ -57,8 +57,8 @@
     \code{TRUE}. This argument makes it possible to use different
     colours and line types for groups. The default is to show all
     groups. }
-  \item{label}{Label the centroid of the hull or the ellipse with the
-    group name.}
+  \item{label}{Label the centre of the points in hull or the ellipse with 
+    the group name.}
   \item{startmark}{plotting characer used to mark the first
     item. The default is to use no mark, and for instance, 
     \code{startmark = 1} will draw a circle.  For other plotting characters,
@@ -104,8 +104,10 @@
   is a list of coordinates of the hull and in \code{ordiellipse} a
   list of covariance matrices and scales used in drawing the
   ellipses. These result objects have a summary method that returns
-  the coordinates of the centroids of the ellipses or hulls and their
-  surface areas in user units.
+  the coordinates of the centres of the ellipses or hulls and their
+  surface areas in user units. The centres of the hulls may differ
+  from the location of the \code{label} which is the centre of the
+  points instead of the centre of the polygon.
 
   Function \code{ordiarrows} draws
   \code{\link{arrows}} and \code{ordisegments} draws line